"Taisuke Boku,Masatake Sugita,Ryohei Kobayashi,Shinnosuke Furuya,Takuya Fujie,Masahito Ohue,Yutaka Akiyama","Improving Performance on Replica-Exchange Molecular Dynamics Simulations by Optimizing GPU Core Utilization","53rd International Conference on Parallel Processing (ICPP2024)","Proceedings of the 53rd International Conference on Parallel Processing (ICPP2024)","Association for Computing Machinery",,,"Page 1082-1091",2024,Aug.
"Masatake Sugita,Takuya Fujie,Yudai Noso,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Development and Application of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations","21st IUPAB and 62nd BSJ joint congress 2024",,"American Chemical Society",,,,2024,June
"杉田 昌岳,藤江 拓哉,能祖 雄大,柳澤 渓甫,大上 雅史,秋山 泰","拡張アンサンブル分子動力学シミュレーションに基づいた環状ペプチドの膜透過性予測技術の開発と応用","第24回日本蛋白質科学会年会",,,,,,2024,June
"赤木 果歩,柳澤 渓甫,秋山 泰","共溶媒分子動力学法による化合物ドッキング向けのバイアス情報の取得","情報処理学会 第148回MPS・第78回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  37","  1-8",2024,June
"清水 正義,柳澤 渓甫,秋山 泰","有望なフラグメント空間配置対に基づく化合物プレスクリーニング手法の開発","情報処理学会 第148回MPS・第78回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  38","  1-8",2024,June
"Keisuke Yanagisawa,Takuya Fujie,Kazuki Takabatake,Yutaka Akiyama","QUBO Problem Formulation of Fragment-Based Protein?Ligand Flexible Docking",,"Entropy","MDPI","  26",,,2024,Apr.
"布部 絢子,柳澤 渓甫,秋山 泰","フラグメントに基づくバーチャルスクリーニングへの利用などを目指したフラグメント集合の選定","情報処理学会 第77回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  31","  1-7",2024,Mar.
"李 佳男,柳澤 渓甫,秋山 泰","CycPeptMP：マルチレベルの分子特徴とデータ拡張による環状ペプチドの膜透過性予測手法の開発","第147回MPS・第77回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  15","  1-8",2024,Mar.
"Masatake Sugita,Takuya Fujie,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Development of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations","The 61st Annual Meeting of The Biophysical Society of Japan",,,,,,2023,Nov.
"Ryunosuke Yoshino,Nobuaki Yasuo,Yohsuke Hagiwara,Takashi Ishida,Daniel Ken Inaoka,Yasushi Amano,Yukihiro Tateishi,Kazuki Ohno,Ichiji Namatame,Tatsuya Niimi,Masaya Orita,Kiyoshi Kita,Yutaka Akiyama,Masakazu Sekijima","Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography",,"ACS omega",,"Vol. 8","No. 29","pp. 25850-25860",2023,July
"齋藤那哉,柳澤渓甫,秋山 泰","フラグメント対の相対位置から検索可能な化合物立体配座データベースの構築","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-74","  37","  1-8",2023,June
"李 佳男,柳澤 渓甫,杉田 昌岳,藤江 拓哉,大上 雅史,秋山 泰","CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  38","  1-8",2023,June
"渡辺銀河,柳澤渓甫,秋山 泰","標的RNAの高次構造予測に基づく低活性ASO候補配列の推測","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-74","  36","  1-8",2023,June
"Masatake Sugita,Takuya Fujie,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations",,"Journal of Chemical Information and Modeling","American Chemical Society","Volume 62","Issue 18","pp. 4549-4560",2022,Sept.
"Keisuke Yanagisawa,Rikuto Kubota,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation",,"ACS Omega","American Chemical Society","Volume 7","Issue 34","pp. 30265-30274",2022,Aug.
"津嶋佑旗,柳澤渓甫,大上雅史,秋山泰","新たなデータセットによる長距離フラグメントリンキング手法の再評価",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  16","  1-8",2022,Mar.
"玉野史結,伊澤和輝,柳澤渓甫,大上雅史,秋山泰","Gapmer型ASOにおけるオフターゲット効果のリスク評価手法の提案",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  7","  1-7",2022,Mar.
"稲垣雅也,柳澤渓甫,大上雅史,秋山泰","フラグメント化された化合物立体構造データベースの構築",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  15","  1-8",2022,Mar.
"山崎眞拓,伊澤和輝,平田稜,柳澤渓甫,大上雅史,秋山泰","結合エネルギーを考慮したゲノムワイドな高速短鎖核酸配列検索手法の開発",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  8","  1-8",2022,Mar.
"Takabatake K,Yanagisawa K,Akiyama Y.","Solving Generalized Polyomino Puzzles Using the Ising Model",,"Entropy","MDPI","Vol. 24","Issue (3)","pp. 354",2022,Feb.
"Jianan Li,Yanagisawa K,Yoshikawa Y,Ohue M,Akiyama Y.","Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning",,"Bioinformatics",,"Volume 38","Issue 4","  1110-1117",2022,Feb.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測","第58回日本生物物理学会年会",,,,,,2021,Nov.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測","第58回日本生物物理学会年会",,,,,,2021,Nov.
"Sugita M,Sugiyama S,Takuya Fujie,Yoshikawa Y,Yanagisawa K,Ohue M,Akiyama Y.","Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations","CBI学会2021年大会",,,,,,2021,Oct.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測","第43回溶液化学シンポジウム",,,,,,2021,Oct.
"Kazuki Takabatake,Kazuki Izawa,Motohiro Akikawa,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Improved Homology Search for Metagenomic Analysis by Two-Step Seed Search with Reduced Amino Acid Alphabets","The 10th International Conference on Bioinformatics and Biomedical Science (ICBBS2021)",,,,,,2021,Oct.
"Masahito Ohue,Kento Aoyama,Yutaka Akiyama","High-performance cloud computing for exhaustive protein-protein docking","The 26th International Conference on Parallel & Distributed Processing (PDPTA’20)","Advances in Parallel & Distributed Processing, and Applications","Springer,cham",,,"pp. 737-746",2021,Oct.
"Takabatake K,Izawa K,Akikawa M,Yanagisawa K,Ohue M,Akiyama Y.","Improved large-scale homology search by two-step seed search using multiple reduced amino acid alphabets",,"Genes",,"  12","  9","  1455",2021,Sept.
"津嶋佑旗,柳澤渓甫,大上雅史,秋山泰.","タンパク質表面との結合親和性を考慮した長距離フラグメントリンキング手法の開発","第67回BIO研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2021-BIO-67","  1","Page 1-8",2021,Sept.
"Masahito Ohue,Hiroki Watanabe,Yutaka Akiyama","MEGADOCK-Web-Mito: human mitochondrial protein-protein interaction prediction database","27th International Conference on Parallel & Distributed Processing (PDPTA’21)","Advances in Parallel & Distributed Processing, and Applications(Accepted)","Springer",,,,2021,July
"Sugita M,Sugiyama S,Takuya Fujie,Yoshikawa Y,Yanagisawa K,Ohue M,Akiyama Y.","Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations",,"Journal of Chemical Information and Modeling",,"  61","  7","  3681-3695",2021,July
"Isawa Kazuya,Yanagisawa Keisuke,Ohue Masahito,Akiyama Yutaka","Antisense oligonucleotide activity analysis based on opening and binding energies to targets","Proceedings of The 27th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’21)","Advances in Parallel & Distributed Processing and Applications",,,,,2021,July
"Masahito Ohue,Yutaka Akiyama","MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions","27th International Conference on Parallel & Distributed Processing (PDPTA’21)","Advances in Parallel & Distributed Processing, and Applications(Accepted)","Springer",,,,2021,July
"Izawa K,Okamoto-Shibayama K,Kita D,Tomita S,Saito A,Ishida T,Ohue M,Akiyama Y,Ishihara K.","Taxonomic and gene category analyses of subgingival plaques from a group of Japanese individuals with and without periodontitis",,"International Journal of Molecular Sciences","International Journal of Molecular Sciences","Volume 22","Issue 10","  5298",2021,May
"Kosuke Fujimoto,Yasumasa Kimura,Jessica R Allegretti,Mako Yamamoto,Yao-zhong Zhang,Kotoe Katayama,Georg Tremmel,Yunosuke Kawaguchi,Masaki Shimohigoshi,Tetsuya Hayashi,Miho Uematsu,Kiyoshi Yamaguchi,Yoichi Furukawa,Yutaka Akiyama,Rui Yamaguchi,Sheila E. Crowe,Peter B. Ernst,Satoru Miyano,Hiroshi Kiyono,Seiya Imoto,Satoshi Uematsu","Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation",,"Gastroenterology","Elsevier","Volume 160","Issue 6","Page 2089-2102.e12",2021,May
"井澤和也,柳澤渓甫,大上雅史,秋山泰","標的配列との結合・開放エネルギー推定に基づくアンチセンス核酸の阻害活性モデルの研究",,"情報処理学会研究報告",,"Vol. 2021-BIO-65","No. 7","pp. 1-7",2021,Mar.
"Fujimoto K,Kimura Y,Shimohigoshi M,Satoh T,Sato S,Tremmel G,Uematsu M,Kawaguchi Y,Usui Y,Hayashi T,Kashima K,Yuki Y,Furukawa Y,Kakuta M,Yutaka Akiyama,Yamaguchi R,Crowe SE,Ernst PB,Miyano S,Kiyono H,Imoto S,Uematsu S","Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts",,"Cell Host & Microbe","Elsevier","Volume 28","Issue 3","Page 380-389",2020,Sept.
"Izawa K,Kubosaki A,Kobayashi N,Akiyama Y,Yamazaki A,Hashimoto K,Konuma R,Kamata Y,Hara-Kudo Y,Hasegawa K,Ikaga T,Watanabe M","Comprehensive Fungal Community Analysis of House Dust Using Next-Generation Sequencing",,"International Journal of Environmental Research and Public Health",,"Volume 17","Issue 16","  5842",2020,Aug.
"大上雅史,青山建人,秋山泰","GPUスパコンによる細胞スケールのタンパク質間相互作用予測","生命情報科学若手の会第12回研究会",,,,,,2020,Aug.
"Aizhen Ren,Takashi Ishida,Yutaka Akiyama","Mathematical proof of the third order accuracy of the speedy double botstrap method",,"Communication in Statistics-Theory and Methods","Taylor & Francis","Vol. 49","issue 16","pp. 3950-3964",2020,Aug.
"Masahito Ohue,Kento Aoyama,Yutaka Akiyama","High-performance cloud computing for exhaustive protein-protein docking",,"IPSJ Technical Report",,"Vol. 2020-MPS-129","No. 6","pp. 1-4",2020,July
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC environments-aware container image configuration workflow for large-scale all-to-all protein-protein docking calculations","The 6th Asian Conference on Supercomputing Frontiers (SCFA2020)","Lecture Notes in Computer Science","Springer","Vol. 12082",,"pp. 23-39",2020,June
"Takuya Fujie,Masatake Sugita,Satoshi Sugiyama,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Conformational Sampling with Molecular Dynamics Simulation for Prediction of Membrane Permeability of Cyclic Peptide","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"高畠和輝,伊澤和輝,秋川元宏,大上雅史,秋山泰","圧縮アミノ酸を利用した二段階のシード探索によるメタゲノム配列相同性検索の改良",,"研究報告バイオ情報学（BIO）",,"Vol. 2020-BIO-61","No. 10","pp. 1-6",2020,Mar.
"村田翔太朗,山田雄太,吉川寧,大上雅史,秋山泰","二次元分子記述子を用いた機械学習による環状ペプチドの細胞膜透過性予測",,"研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2020-BIO-61","No. 5","pp. 1-7",2020,Mar.
"久保田陸人,柳澤渓甫,吉川寧,大上雅史,秋山泰","共通な部分構造の再利用による高速なタンパク質リガンドドッキング手法の開発",,"情報処理学会研究報告",,"Vol. 2020-BIO-61","No. 4","pp. 1-8",2020,Mar.
"渡辺紘生,大上雅史,秋山泰","マルチノード・マルチGPU上での網羅的なタンパク質間相互作用予測の高速化",,"情報処理学会研究報告","情報処理学会","Vol. 2020-BIO-61","No. 3","pp. 1-8",2020,Mar.
"Kazuki Izawa,K Shibayama,Masahito Ohue,Takashi Ishida,Kazuyuki Ishihara,Yutaka Akiyama","The shifts in bacterial community and gene category composition between healthy sites and periodontal disease sites","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Masaya Inagaki,Masahito Ohue,Yutaka Akiyama","Fragment Linking with DQN","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Yuki Tsushima,Masahito Ohue,Yutaka Akiyama","Development of fragment linking method for beyond rule of five","The 5th IITM-Tokyo Tech Joint Symposium-Current trends in Bioinformatics: Big data analysis, machine learning and drug design",,,,,,2020,Mar.
"Masahito Ohue,Shogo D. Suzuki,Yutaka Akiyama","PKRank & SPDRank - Learning-to-rank methods for machine-learning-based drug discovery","Biophysical Society 64th Annual Meeting",,,,,,2020,Feb.
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Shunpei Matsuno,Masahito Ohue,Yutaka Akiyama","Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Satoshi Sugiyama,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Development of Membrane Permeability Prediction System for Cyclic Peptide: Large-Scale Molecular Dynamics Simulations","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Max Druyvesteyn,Masahito Ohue,Yutaka Akiyama","Improved protein-protein docking using arbitrary docking-derived protein interface predictions","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Li Jianan,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Prediction of plasma protein binding for cyclic peptides by deep learning and molecular docking","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Exhaustive protein-protein interaction prediction using MEGADOCK on a large-scale HPC environment","2nd RWBC-OIL Workshop",,,,,,2020,Jan.
"Shumpei Matsuno,Masahito Ohue,Yutaka Akiyama","Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces",,"Biophysics and Physicobiology",,"Vol. 17",,"pp. 2-13",2020,Jan.
"Kento Aoyama,Masanori Kakuta,Yuri Matsuzaki,Takashi Ishida,Masahito Ohue,Yutaka Akiyama","Development of computational pipeline software for genome/exome analysis on the K computer",,"Supercomputing Frontiers and Innovations",,"Vol. 7","No. 1","pp. 37-54",2020,
"Shuntaro Chiba,Masahito Ohue,Anastasiia Gryniukova,Petro Borysko,Sergey Zozulya,Nobuaki Yasuo,Ryunosuke Yoshino,Kazuyoshi Ikeda,Woong-Hee Shin,Daisuke Kihara,Mitsuo Iwadate,Hideaki Umeyama,Takaaki Ichikawa,Reiji Teramoto,Kun-Yi Hsin,Vipul Gupta,Hiroaki Kitano,Mika Sakamoto,Akiko Higuchi,Nobuaki Miura,Kei Yura,Masahiro Mochizuki,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,M. Michael Gromiha,Itsuo Nakane,Nanako Uchida,Hayase Hakariya,Modong Tan,Hironori Nakamura,Shogo Suzuki,Tomoki Ito,Masahiro Kawatani,Kentaroh Kudoh,Sakurako Takashina,Kazuki Yamamoto,Yoshitaka Moriwaki,Keita Oda,Daisuke Kobayashi,Tatsuya Okuno,Shintaro Minami,George Chikenji,Philip Prathipati,Chioko Nagao,Attayeb Mohsen,Mari Ito,Kenji Mizuguchi,Teruki Honma,Takashi Ishida,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima.","A prospective compound screening contest identified broader inhibitors for Sirtuin 1",,"Scientific Reports",,"  9",,,2019,Dec.
"Keren Jiang,Di Zhang,Tsubasa Iino,Risa Kimura,Tatsuo Nakajima,Kana Shimizu,Masahito Ohue,Yutaka Akiyama.","A playful tool for predicting protein-protein docking","Mobile and Ubiquitous Multimedia (MUM 2019)","In Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia (MUM 2019)","ACM",,"No. 40","Page 1-5",2019,Nov.
"Ohue M,Shogo Suzuki,Akiyama Y.","Learning-to-rank technique based on ignoring meaningless ranking orders between compounds",,"Journal of Molecular Graphics and Modelling","Elsevier","Volume 92",,"pp. 192-200",2019,Nov.
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application","International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'19)",,,,,,2019,Nov.
"大上雅史,鈴木翔吾,秋山泰","PKRank & SPDRank 化合物選別のためのランク学習法","生命情報科学若手の会第11回研究会",,,,,,2019,Oct.
"Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Accelerating MEGADOCK: protein-protein interaction prediction software on multiple nodes and multiple GPUs environment","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Masahito Ohue,Hiroki Watanabe,Kento Aoyama,Yutaka Akiyama","Acceleration and virtualization of parallel protein-protein interaction prediction system MEGADOCK","The 57th Annual Meeting of the Biophysical Society of Japan",,,,,,2019,Sept.
"Masahito Ohue,Shogo D. Suzuki,Yutaka Akiyama","PKRank & SPDRank: Learning-to-rank methods for ligand-based virtual screening","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Kento Aoyama,Hiroki Watanabe,Masahito Ohue,Yutaka Akiyama","Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Yuta Yamada,Yasushi Yoshikawa,Naoki Wakui,Masahito Ohue,Yutaka Akiyama","Development of Membrane Permeability Prediction Method for Cyclic Peptids with Machine Learning","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Kazuki Izawa,Kazuki Shibayama,Masahito Ohue,Kazuyuki Ishihara,Yutaka Akiyama","Bacterial community and gene category composition analysis with high-speed homology search tool suggests the difference between periodontal disease and healthy sites","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Shumpei Matsuno,Masahito Ohue,Yutaka Akiyama","Multidomain protein structure prediction using multimeric interaction residue pair information","第8回生命医薬情報学連合大会 (IIBMP2019)",,,,,,2019,Sept.
"Masahito Ohue,Marina Yamasawa,Kazuki Izawa,Yutaka Akiyama","Parallelized pipeline for whole genome shotgun metagenomics with GHOSTZ-GPU and MEGAN","In Proceedings of the 19th annual IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2019)",,"IEEE",,,"  152-156",2019,Aug.
"Ohue M,Ii R,Yanagisawa K,Akiyama Y.","Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph",,"IPSJ SIG Technical Report",,"Vol. 2019-MPS-124","No. 3","pp. 1-4",2019,July
"Aoyama K,Yamamoto Y,Ohue M,Akiyama Y.","Performance evaluation of MEGADOCK protein?protein interaction prediction system implemented with distributed containers on a cloud computing environment","Parallel and Distributed Processing Techniques and Applications （PDPTA'19）","In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)",,,,"pp. 175-181",2019,July
"Aoyama K,Yamamoto Y,Ohue M,Akiyama Y.","Performance evaluation of MEGADOCK protein?protein interaction prediction system implemented with distributed containers on a cloud computing environment",,"IPSJ SIG Technical Report",,"Vol. 2019-MPS-124","No. 13","pp. 1-4",2019,July
"Ohue M,Ii R,Yanagisawa K,Akiyama Y.","Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph","Parallel and Distributed Processing Techniques and Applications （PDPTA'19）","In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)",,,,"Page 122-128",2019,July
"Ban T,Ohue M,Akiyama Y.","NRLMFβ: Bata-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization for Improving Performance of Drug?Target Interaction Prediction",,"Biochemistry and Biophysics Reports","Elsevier","Volume 18",,,2019,July
"松野駿平,大上雅史,秋山泰.","マルチドメインタンパク質の相互作用残基ペア予測を用いた立体構造予測手法の改良","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-58","No. 53","pp. 1-7",2019,June
"李佳男,吉川寧,大上雅史,秋山泰.","機械学習を用いた環状ペプチドの体内安定性予測手法の改良","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）",,"Vol. 2019-BIO-58","No. 52","pp. 1-8",2019,June
"木曽良明,秋山 泰,大上 雅史,吉川 寧,和久井 直樹","中分子創薬に適した特性を有する環状ペプチドのインシリコ設計（第8章）",,"木曽良明監修「ペプチド創薬の最前線」","シーエムシー出版",,,"pp. 70-78",2019,May
"大上雅史,林孝紀,秋山泰","タンパク質間相互作用と複合体構造の予測結果を検索できるウェブサイト「MEGADOCK-Web」",,"実験医学 2019年6月号","羊土社","Vol. 37","No. 9","pp. 1469-1474",2019,May
"Masahito Ohue,Takanori Hayashi,Yuri Matsuzaki,Keisuke Yanagisawa,Yutaka Akiyama","Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions","Biophysical Society 63rd Annual Meeting",,,,,,2019,Mar.
"黄毅聰,吉川寧,和久井直樹,大上雅史,秋山泰.","拡張サンプリング法による環状ペプチドの膜透過性予測システムの構築","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 10","pp. 1-8",2019,Mar.
"伊井 良太,柳澤 渓甫,大上 雅史,秋山 泰","分子グラフ上の距離を考慮したグラフ畳込みニューラルネットワークによる化合物活性予測","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 11","pp. 1-8",2019,Mar.
"林 孝紀,大上 雅史,秋山 泰.","代表タンパク質構造群との構造アラインメントスコアプロファイルに基づくタンパク質間相互作用予測の高速化","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 12","pp. 1-8",2019,Mar.
"山田 雄太,吉川 寧,和久井 直樹,大上 雅史,秋山 泰","機械学習を用いた環状ペプチドの膜透過性予測手法の開発","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 13","pp. 1-8",2019,Mar.
"Takashi Tajimi,Naoki Wakui,Keisuke Yanagisawa,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques",,"BMC Bioinformatics","Springer Nature","Volume 19",,,2018,Dec.
"Takashi Tajimi,Naoki Wakui,Keisuke Yanagisawa,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques","the 29th International Conference on Genome Informatics (GIW 2018)","BMC Bioinformatics","Springer Nature","Volume 19",,,2018,Dec.
"Naomi Wakayama,Kota Toshimoto,Kazuya Maeda,Shun Hotta,Takashi Ishida,Yutaka Akiyama,Yuichi Sugiyama","In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines",,"Pharmaceutical Research","Springer US","  35:197","  10","pp. 1-21",2018,Oct.
"Masahito Ohue,Takanori Hayashi,Hiroki Watanabe,Yuri Matsuzaki,Nobuyuki Uchikoga,Yutaka Akiyama","Supercomputing-based exhaustive protein-protein interaction prediction and its open database.","The 56th Annual Meeting of the Biophysical Society of Japan",,,,,,2018,Sept.
"Wakayama N,Toshimoto K,Maeda K,Hotta S,Ishida T,Akiyama Y,Sugiyama Y.","In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines",,"Pharmaceutical Research",,,,,2018,Aug.
"Masahiro Mochizuki,Shogo Suzuki,Yanagisawa K,Ohue M,Akiyama Y.","QEX: target-specific druglikeness filter enhances ligand-based virtual screening",,"Molecular Diversity","Springer","Volume 23","issue 1","pp. 11-18",2018,July
"久保田陸人,柳澤渓甫,大上雅史,秋山泰","共通な部分構造の再利用アルゴリズムを用いたタンパク質リガンドドッキング手法の開発","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54(42)",,"  1-8",2018,June
"Shogo Suzuki,Masahito Ohue,Yutaka Akiyama","PKRank: a novel learning-to-rank method for ligand-based virtual screening using pairwise kernel and RankSVM",,"Artificial Life and Robotics","Springer Japan","  23","  2","  205-212",2018,June
"Yanagisawa K,Komine S,Kubota R,Ohue M,Akiyama Y.","Optimization of memory use of fragment extension-based protein?ligand docking with an original fast minimum cost flow algorithm",,"Computational Biology and Chemistry (In Proc. APBC2018)",,"Volume 74",,"Page 399-406",2018,June
"青山健人,大上雅史,秋山泰","生命情報解析分野におけるコンテナ型仮想化技術の動向と性能検証","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54","  47","  1-7",2018,June
"渡辺紘生,林孝紀,大上雅史,秋山泰","ミトコンドリアに関連したヒトタンパク質間相互作用予測データベースMEGADOCK-Web-Mitoの開発","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54","  46","  1-8",2018,June
"多治見隆志,和久井直樹,大上雅史,秋山泰","複数のLasso回帰解に基づく解釈性の良い予測モデルを目指した環状ペプチド医薬品の体内安定性予測","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54","  45","  1-8",2018,June
"Hayashi T,Matsuzaki Y,Yanagisawa K,Ohue M,Akiyama Y.","MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions",,"BMC Bioinformatics (In Proc. APBC2018)",,"  19","  (Suppl 4)","  62",2018,May
"Ban T,Masahito O,Yutaka Akiyama","Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem",,"Computational Biology and Chemistry",,"Volume 73",,"Page 139-146",2018,Apr.
"山本悠生,大上雅史,秋山泰.","クラウド上の分散GPU環境におけるタンパク質間相互作用予測計算フレームワークの開発","情報処理学会 第53回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-53","  8","  1-8",2018,Mar.
"後藤公太,大上雅史,石田貴士,秋山泰","配列相同性検索ツールGHOSTZ-GPUのMPI環境における高速化","情報処理学会 第53回バイオ情報学研究会","情報処理学会研究報告",,"  2017-BIO-53","  7","  1-8",2018,Mar.
"後藤公太,大上雅史,石田貴士,秋山泰","配列相同性検索ツールGHOSTZ-GPUのMPI環境における高速化","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-53","  7","  1-8",2018,Mar.
"山本悠生,大上雅史,秋山泰","クラウド上の分散GPU環境におけるタンパク質間相互作用予測計算フレームワークの開発","情報処理学会研究報告 バイオ情報学（BIO）",,,"  2018-BIO-53(8)",,,2018,Mar.
"Ramakrishnan C,Thangakani AM,Velmurugan D,Krishnan DA,Sekijima M,Akiyama Y,Gromiha MM.","Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques",,"Journal of Biomolecular Structure and Dynamics",,"Volume 36","  Issue 6","Page 1566-1576",2018,
"Masahito Ohue,Yuki Yamamoto,Kento Aoyama,Yutaka Akiyama","MEGADOCK-Azure: high-performance protein-protein docking on Microsoft Azure HPC","4th IIT Madras-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics: Large Scale Data Analysis, Resources and Drug Design",,,,,,2017,Nov.
"Ban T,Ohue M,Akiyama Y","Efficient Hyperparameter Optimization by Using Bayesian Optimization for Drug-Target Interaction Prediction","In Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017)",,"IEEE",,,,2017,Oct.
"Masanori Kakuta,Shuji Suzuki,Kazuki Izawa,Takashi Ishida,Yutaka Akiyama","A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data",,"International Journal of Molecular Sciences","Multidisciplinary Digital Publishing Institute","Vol. 18","No. 10","pp. 2124",2017,Oct.
"Shuntaro Chiba,Takashi Ishida,Kazuyoshi Ikeda,Masahiro Mochizuki,Reiji Teramoto,Y-h. Taguchi,Mitsuo Iwadate,Hideaki Umeyama,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,M. Michael Gromiha,Tatsuya Okuno,Koya Kato,Shintaro Minami,George Chikenji,Shogo D. Suzuki,Keisuke Yanagisawa,Woong-Hee Shin,Daisuke Kihara,Kazuki Z. Yamamoto,Yoshitaka Moriwaki,Nobuaki Yasuo,Ryunosuke Yoshino,Sergey Zozulya,Petro Borysko,Roman Stavniichuk,Teruki Honma,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima","An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes",,"Scientific Reports","Nature Publishing Group","Vol. 7","No. 12038","pp. 1-13",2017,Sept.
"Ohue M,Yamazaki T,Ban T,Akiyama Y","Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach","Intelligent Computing Theories and Application (In Proceedings of ICIC2017, Lecture Notes in Computer Science)","Lecture Notes in Computer Science","Springer, Cham","Vol. 10362",,"pp. 549-558",2017,Aug.
"Ryunosuke Yoshino,Nobuaki Yasuo,Yohsuke Hagiwara,Takashi Ishida,Daniel Ken Inaoka,Yasushi Amano,Yukihiro Tateishi,Kazuki Ohno,Ichiji Namatame,Tatsuya Niimi,Masaya Orita,Kiyoshi Kita,Yutaka Akiyama,Masakazu Sekijima","In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease",,"Scientific Reports","Springer Nature","  7",,,2017,July
"山澤 まりな,伊澤 和輝,大上 雅史,石田 貴士,Kazuyuki Ishihara,秋山 泰","高速相同性解析ツールGHOSTXを用いた口腔内メタゲノム解析","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  41","  1-7",2017,June
"伊澤 和輝,山澤 まりな,大上 雅史,石田 貴士,秋山 泰","歯周病の発症要因の特定に向けた口腔内細菌叢解析","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  40","  1-6",2017,June
"林孝紀,山本悠生,松崎由理,大上雅史,秋山泰","タンパク質間相互作用予測統合データベースMEGADOCK-WEBの改良とクラウド計算環境との連携","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  39","  1-8",2017,June
"柳澤渓甫,小峰駿汰,久保田陸人,大上雅史,秋山泰","フラグメント伸長型化合物ドッキング計算のための重み付きオフラインキャッシュ問題の厳密解アルゴリズム","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  38","  1-8",2017,June
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Yutaka Akiyama","Rigid-Docking Approaches to Explore Protein?Protein Interaction Space",,"Advances in Biochemical Engineering/Biotechnology(Network Biology)","Springer, Cham","volume 160",,"pp. 33-35",2017,May
"Shuji Suzuki,Takashi Ishida,Masahito Ohue,Masanori Kakuta,Yutaka Akiyama","GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data",,"Methods in Molecular Biology(Protein Function Prediction)","Springer","Volume 1611",,"pp. 15-25",2017,Apr.
"大上 雅史,山本 悠生,秋山 泰","Microsoft Azure上でのタンパク質間相互作用予測システムの並列計算と性能評価","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）",,"  2017-BIO-49","  4","  1-3",2017,Mar.
"青山 健人,山本 悠生,大上 雅史,秋山 泰","コンテナ型仮想化による分散計算環境におけるタンパク質間相互作用予測システムの性能評価","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-49","  3","  1-8",2017,Mar.
"柳澤渓甫,大上雅史,石田貴士,秋山泰","標的タンパク質の立体構造を用いたリガンド候補化合物の上限サイズの推定による化合物フィルタリング","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）",,"  2017-BIO-49","  6","  1-7",2017,Mar.
"Yanagisawa K,Komine S,Shogo Suzuki,Ohue M,Ishida T,Akiyama Y.","Spresso: an ultrafast compound pre-screening method based on compound decomposition",,"Bioinformatics","OXFORD Academic","Volume 33","Issue 23","Page 3836-3843",2017,Mar.
"Masahito Ohue,Yamamoto, Yuki,Hayashi, Takanori,Yuri Matsuzaki,Yutaka Akiyama","Cloud Computing for All-To-All Protein-Protein Docking on Azure HPC","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 451A-451A",2017,Feb.
"Yuri Matsuzaki,Simm, Jaak,Uchikoga, Nobuyuki,Yutaka Akiyama","A Docking Based Approach to Analyze Interaction Surfaces of Virus-Host Protein-Protein Interactions","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 451A-452A",2017,Feb.
"Uchikoga, Nobuyuki,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Interaction Surfaces of Proteins Involved in Bacterial Chemotaxis with Rigid-Body Docking Decoys","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 290A-290A",2017,Feb.
"Shogo Suzuki,Masahito Ohue,Yutaka Akiyama","Learning-to-rank based compound virtual screening by using pairwise kernel with multiple heterogeneous experimental data","22nd International Symposium on Artifical Life and Robotics",,,,,"  114-119",2017,Jan.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method with segmented compounds","Chem-Bio Informatics Society(CBI) Annual Meeting 2016",,,,,,2016,Oct.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition","The 27th International Conference on Genome Informatics (GIW 2016)",,,,,,2016,Oct.
"Masahito Ohue,Yuki Yamamoto,Hiroyuki Sato,Takashi Matsushita,Yutaka Akiyama","MEGADOCK-Azure: High-performance protein-protein interaction prediction system on Microsoft Azure HPC","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Kota Goto,Kota Kasahara,Masahito Ohue,Haruki Nakamura,Yutaka Akiyama","Accelerating SHAKE Calculation of myPresto/omegagene Molecular Dynamics Simulation on CPU/GPU heterogeneous environment","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Marina Yamasawa,Tomoya Fujii,Kota Goto,Masahito Ohue,Takashi Ishida,Kazuyuki Ishihara,Yutaka Akiyama","GPU/MPI Parallelization of Metagenomic Sequence Homology Search Tool and Its Application to Oral Metagenomics","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Takanori Hayashi,Kazuki Nagasawa,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","MEGADOCK-WEB: a database of predicted protein-protein interactions and its web interface","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Shogo Suzuki,Masahito Ohue,Yutaka Akiyama","Learning to Rank with Ignoring Meaningless Order and Its Application to Virtual Screening for Drug Discovery","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound segmentation","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Kota Kasahara,Benson Ma,Kota Goto,Bhaskar Dasgupta,Junichi Higo,Ikuo Fukuda,Tadaaki Mashimo,Yutaka Akiyama,Haruki Nakamura","myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme",,"Biophysics and Physicobiology",,"Vol. 13（2016）",,"p. 209-216",2016,Aug.
"Shuji Suzuki,Masanori Kakuta,Takashi Ishida,Yutaka Akiyama","GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering",,"PLOS ONE",,"Vol. 11","No. 8","  e0157338",2016,Aug.
"秋山 泰","アミノ酸配列に対する高速な配列相同性検索（GHOSTXおよび並列版GHOST-MP）","第一回マイクロプロテイン研究会",,,,,,2016,July
"Yutaka Akiyama","Massively parallel bioinformatics computing  on K-computer, TSUBAME, and Azure:  Metagenome analysis and exhaustive protein-protein interaction prediction","ICR seminar",,,,,,2016,July
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Specificity of broad protein interaction surfaces for proteins with multiple binding partners",,"Biophysics and Physicobiology","THE BIOPHYSICAL SOCIETY OF JAPAN","Vol. 13",,"pp. 105-115",2016,July
"Atsushi Ose,Kota Toshimoto,Kazushi Ikeda,Kazuya Maeda,Shuya Yoshida,Fumiyoshi Yamashita,Mitsuru Hashida,Takashi Ishida,Yutaka Akiyama,Yuichi Sugiyama","Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure",,"Journal of Pharmaceutical Sciences",,"Vol. 105","No. 77","p. 2222-2230",2016,July
"青山 健人,角田 将典,松崎 由理,石田 貴士,秋山 泰","スーパーコンピュータ「京」上でのエクソーム解析パイプラインの開発",,"情報処理学会論文誌コンピューティングシステム（ACS）",,"Vol. 9","No. 2","p. 15-33",2016,July
"後藤 公太,笠原 浩太,大上 雅史,中村 春木,秋山 泰","SHAKE法に着目した分子動力学ソフトウェアmyPresto/OmegageneのCPU・GPU混在環境における高速化","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  17","  1-7",2016,June
"鈴木 翔吾,大上 雅史,秋山 泰","活性値情報のグループ化とランク学習による化合物スクリーニング","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  26","  1-7",2016,June
"柳澤 渓甫,小峰 駿汰,鈴木 翔吾,大上 雅史,石田 貴士,秋山 泰","フラグメント分割に基づく超高速化合物プレスクリーニング手法ESPRESSO","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  18","  1-7",2016,June
"秋山 泰","Azure上での1000コア級並列計算 ?生命情報解析の共通基盤を目指して","学術情報基盤オープンフォーラム２０１６","http://www.nii.ac.jp/csi/openforum2016/track/day2_5.html#period1",,,,,2016,May
"藤井智也,角田将典,大上雅史,石田貴士,石原和幸,秋山泰","GPUを用いたメタゲノム配列相同性解析ツールのMPI並列化と応用",,"研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  3","  1-4",2016,Mar.
"長澤一輝,松崎由理,大上雅史,秋山泰","タンパク質間相互作用予測結果データベース及び表示系の構築","情報処理学会 第45回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  2","  1-4",2016,Mar.
"山崎卓朗,大上雅史,秋山泰","タンパク質-化合物相互作用ネットワークのリンクマイニング","情報処理学会 第45回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-45","  9","  1-7",2016,Mar.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"Masahito Ohue,Yutaka Akiyama","A rescoring method of protein-peptide docking prediction with amino acid profiles of rigid-body search results","The Fourteenth Asia Pacific Bioinformatics Conference (APBC2016)",,,,,,2016,Jan.
"Yutaka Akiyama","GHOST-MP:  an ultra-fast and high-sensitive homology search tool for metagenome analysis","ADAC Workshop",,,,,,2016,Jan.
"大上雅史,松崎由理,石田貴士,秋山泰","タンパク質間相互作用予測システムMEGADOCKによるEGFRパスウェイ解析","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"Shuntaro Chiba,Kazuyoshi Ikeda,Takashi Ishida,M. Michael Gromiha,Y-h. Taguchi,Mitsuo Iwadate,Hideaki Umeyama,Kun-Yi Hsin,Hiroaki Kitano,Kazuki Yamamoto,Nobuyoshi Sugaya,Koya Kato,Tatsuya Okuno,George Chikenji,Masahiro Mochizuki,Nobuaki Yasuo,Ryunosuke Yoshino,Keisuke Yanagisawa,Tomohiro Ban,Reiji Teramoto,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,Philip Prathipati,Junichi Ito,Yuko Tsuchiya,Kenji Mizuguchi,Teruki Honma,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima","Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target",,"Scientific Reports",,"Vol. 5","No. 17209",,2015,Nov.
"年本広太,尾瀬淳,池田和史,前田和哉,石田貴士,秋山泰,杉山 雄一","機械学習を用いた薬物トランスポーター基質のin silico予測","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Takashi Ishida,Yutaka Akiyama","A comparative study of GPU and MIC accelerations in fast Fourier transform-based protein-protein docking","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Tomohiro Ban,Masahito Ohue,Yutaka Akiyama","Improving protein-ligand docking and inverse docking prediction by deepening conformation search on multiple grids","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound fragmentation","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"鈴木翔吾,大上雅史,秋山泰","活性値情報のグループ化とランク学習による活性化合物予測","第18回情報論的学習理論ワークショップ (IBIS2015)",,,,,,2015,Nov.
"柳澤 渓甫,小峰 駿汰,大上 雅史,石田 貴士,秋山 泰","Fast pre-filtering for virtual screening based on ligand decomposition","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"鈴木翔吾,大上雅史,秋山泰","活性値情報のグループ化を用いたランク学習による化合物スクリーニング","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"伴 兼弘,大上 雅史,秋山 泰","Multiple Grids Arrangement for Improving Conformational Search of Protein-Ligand Docking and Its Application to Inverse Docking Problem","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"Uchikoga, Nobuyuki,Masahito Ohue,Yuri Matsuzaki,Yutaka Akiyama","Post-docking analysis by physicochemical properties of protein-protein interactions generated from rigid-body docking processes","29th Annual Symposium of the Protein-Society","PROTEIN SCIENCE","WILEY-BLACKWELL","Vol. 24",,"pp. 253-253",2015,Oct.
"秋山 泰","次世代シークエンサデータ解析のための情報処理システムの開発","HPCI戦略プログラム分野１成果報告会",,,,,,2015,Oct.
"Tomohiro Ban,Masahito Ohue,Yutaka Akiyama","Multiple Grids Arrangement for Ligand Docking and Its Application to Inverse Docking Problem","IIBMP2015",,,,,,2015,Oct.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound decomposition","IIBMP2015",,,,,,2015,Oct.
"内古閑伸之,松崎由理,大上雅史,秋山泰","剛体アンサンブルドッキングによって得られた候補構造群における相互作用残基ペアの特徴の解析","第53回日本生物物理学会年会",,,,,,2015,Sept.
"大上雅史,内古閑伸之,松崎由理,秋山泰","アミノ酸プロファイルによるタンパク質ペプチド複合体のポストドッキング解析","第53回日本生物物理学会年会",,,,,,2015,Sept.
"秋山泰","バイオインフォマティクス入門",,,"慶應義塾大学出版会",,,,2015,Aug.
"Keisuke Yanagisawa,Takashi Ishida,Yutaka Akiyama","Drug Clearance Pathway Prediction Based on Semi-supervised Learning",,"IPSJ Transactions on Bioinformatics",,"Vol. 8",,"pp. 21-27",2015,Aug.
"大上雅史,内古閑伸之,松崎由理,秋山泰","タンパク質間相互作用残基の物理化学的性質による単純化プロファイルを用いたポストドッキング解析","第15回日本蛋白質科学会年会",,,,,,2015,June
"年本広太,尾瀬淳,池田和史,前田和哉,石田貴士,秋山泰,杉山雄一","機械学習を用いた薬物トランスポーター基質のin silico予測","第10回トランスポーター研究会年会","トランスポーター研究会年会抄録集",,"Vol. 10",,"pp. 78",2015,June
"鈴木翔吾,柳澤渓甫,大上雅史,石田貴士,秋山泰","SVMとDeep Learningに基づくヒトc-Yesキナーゼ阻害化合物の予測","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  36","  1-7",2015,June
"和久井直樹,大上雅史,千葉峻太朗,石田貴士,岩?博史,秋山泰","既知の活性／非活性化合物のドッキング解析によるバーチャルスクリーニングに適したタンパク質立体構造モデルの選択","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  60","  1-4",2015,June
"Yutaka Akiyama,Takashi Ishida","iNTRODB and its Applicationin anti-Trypanosome Drug Discovery","ISNTD d3 2015",,,,,,2015,May
"Suzuki S,Kakuta M,Ishida T,Akiyama Y.","Faster sequence homology searches by clustering subsequences",,"Bioinformatics",,"  31","  8","  1183-90",2015,Apr.
"小幡 康文,石田貴士,秋山泰","タンパク質ドッキングと配列情報特徴解析の融合によるタンパク質間相互作用予測の高精度化",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2015","No. 14","pp. 1-6",2015,Mar.
"Shuji Suzuki,Masanori Kakuta,Takashi Ishida,Yutaka Akiyama","GHOSTZ-GPU: Fast Protein Sequence Homology Search on GPUs","GPU Technology Conference 2015 (GTC2015)",,,,"No. P5273",,2015,Mar.
"相澤 洋輔,石田貴士,秋山泰","ディープラーニングを利用したタンパク質天然変性領域予測",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2015","No. 13","pp. 1-6",2015,Mar.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking","Biophysical Society 59th Annual Meeting",,,,,,2015,Feb.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Yutaka Akiyama","Prediction of human-virus protein-protein interactions by exhaustive rigid docking.","Biophysical Society 59th Annual Meeting",,,,,,2015,Feb.
"Masahito Ohue,Takehiro Shimoda,Shuji suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra?high-performance protein-protein docking software for heterogeneous supercomputers","APBC 2015: The Thirteenth Asia Pacific Bioinformatics Conference",,,,,,2015,Jan.
"Takehiro Shimoda,Shuji Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama.","Protein-Protein Docking on Hardware Accelerators : Comparison of GPU and MIC Architectures","The Thirteenth Asia-Pacific Bioinformatics Conference (APBC2015)","BMC Systems Biology","BioMed Central","Vol. 9","No. Suppl 1",,2015,Jan.
"Kakuta, M.,Suzuki, S.,Ishida, T.,Akiyama, Y.","GHOST-MP: A Massively Parallel Biological Sequence Similarity Search for Metagenomics using OpenMP and MPI","Annual Meeting on Advanced Computing System and Infrastructure (ACSI) 2015",,,,,,2015,Jan.
"Zhang Chaojie,Koichi Shirahata,Shuji Suzuki,Yutaka Akiyama,Satoshi Matsuoka","Performance Analysis of MapReduce Implementations for High Performance Homology Search","HPCS2015",,,,,,2015,
"小峰駿汰,石田貴士,秋山泰","フラグメント伸長型タンパク質-化合物ドッキングのビームサーチによる高速化","情報処理学会 第42回バイオ情報学研究会","情報処理学会研究報告",,,,,2015,
"杉原舜,石田貴士,秋山泰","低分子化合物二次元構造比較システムの改良","情報処理学会 第42回バイオ情報学研究会","情報処理学会研究報告",,,,,2015,
"Masahiro Yano,Hiroshi Mori,Yutaka Akiyama,Takuji Yamada,Ken Kurokawa","CLAST: CUDA implemented large-scale alignment search tool",,"BMC Bioinformatics 2014",,"  15","  406",,2014,Dec.
"年本 広太,若山 直美,堀田駿,前田 和哉,石田 貴士,秋山 泰,杉山 雄一","機械学習を用いた 9 つの主要な in vivo 薬物クリアランス経路の in silico 予測","日本動物実験代替法学会 第27回大会",,,,,,2014,Dec.
"Masahito Ohue,Takehiro Shimoda,Shuji suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra?high-performance protein-protein docking software for heterogeneous supercomputers","GIW/ISCB-Asia 2014",,,,,,2014,Dec.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments","The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014)",,,,,,2014,Nov.
"Takashi Ishida,Kozue Hasumi,Yutaka Akiyama","iNTRODB: database for NTDs drug target protein selection","The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014)",,,,,,2014,Nov.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers","IIBMP2014","Bioinformatics",,"Volume 30","Issue 22","page 3281-3283",2014,Nov.
"大上雅史,松崎由理,石田貴士,秋山泰","タンパク質とペプチドのドッキング計算","生命情報科学若手の会 第6回研究会",,,,,,2014,Oct.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments","Biophysical Society Thematic Meeting Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations",,,,,,2014,Sept.
"大上雅史,松崎由理,内古閑伸之,石田貴士,秋山泰","MEGADOCK: a high-performance protein-protein interaction prediction tool on supercomputing environments","第52回日本生物物理学会年会",,,,,,2014,Sept.
"内古閑伸之,松崎由理,大上雅史,広川貴次,秋山泰","Analysis of properties of protein-protein interaction surface areas involved in more near-native conmplexes by Re-docking scheme","第52回日本生物物理学会年会",,,,,,2014,Sept.
"Suzuki, S,Ishida, T,Akiyama, Y","GHOSTX: An improved sequence homology search algorithm using a query suffix array and a database suffix array",,"PLoS ONE",,"Vol. 6","No. 9","  e103833",2014,Aug.
"Yuki Komatsu,Takashi Ishida,Yutaka Akiyama","Metagenomic Phylogenetic Classification Using Improved Na?ve Bayes","the Tenth International Conference on Intelligent Computing (ICIC 2014)",,,,,,2014,Aug.
"Ohue, M.,Shimoda, T.,Suzuki, S.,Matsuzaki, Y.,Ishida, T.,Akiyama, Y.","MEGADOCK 4.0: an ultra?high-performance protein?protein docking software for heterogeneous supercomputers",,"Bioinformatics","Oxford University Press","Vol. 30","No. 22","pp. 3281-3283",2014,Aug.
"Ban, T.,Ishida, T.,Akiyama, Y.","Improvement of a conformational search on protein-ligand docking based on optimal arrangement of multiple small search grids","The 2014 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'14)",,,,,,2014,July
"大上 雅史,下田 雄大,松崎由理,石田 貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム (情報論的学習理論と機械学習)",,"電子情報通信学会技術研究報告 = IEICE technical report : 信学技報","一般社団法人電子情報通信学会","Vol. 114","No. 105","pp. 173-176",2014,June
"柳澤 渓甫,石田 貴士,秋山泰","半教師付き学習を用いた薬物クリアランス経路予測 (情報論的学習理論と機械学習)",,"電子情報通信学会技術研究報告 = IEICE technical report : 信学技報","一般社団法人電子情報通信学会","Vol. 114","No. 105","pp. 55-60",2014,June
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data",,"Protein and Peptide Letters","Bentham Science","Volume 21","Issue 8","Page 766-778",2014,June
"大上雅史,下田 雄大,松崎由理,石田貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2014-BIO-38","No. 32","pp. 1-4",2014,June
"柳澤 渓甫,石田貴士,秋山泰","半教師付き学習を用いた薬物クリアランス経路予測 (ニューロコンピューティング)",,"電子情報通信学会技術研究報告 = IEICE technical report : 信学技報","一般社団法人電子情報通信学会","Vol. 114","No. 104","pp. 55-60",2014,June
"柳澤 渓甫,石田貴士,秋山泰","半教師付き学習を用いた薬物クリアランス経路予測",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2014","No. 10","pp. 1-6",2014,June
"大上 雅史,下田 雄大,松崎由理,石田貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム (ニューロコンピューティング)",,"電子情報通信学会技術研究報告 = IEICE technical report : 信学技報","一般社団法人電子情報通信学会","Vol. 114","No. 104","pp. 173-176",2014,June
"柳澤 渓甫,石田 貴士,秋山泰","半教師付き学習を用いた薬物クリアランス経路予測",,"研究報告数理モデル化と問題解決（MPS）","一般社団法人情報処理学会","Vol. 2014","No. 10","pp. 1-6",2014,June
"蓮実 梢,石田 貴士,秋山 泰","パスウェイ情報を用いた顧みられない熱帯病 創薬支援のための統合データベースiNTRODBの改良","情報処理学会 第38回バイオ情報学研究会","情報処理学会研究報告",,"  2014-BIO-38",,,2014,June
"青山 健人,角田 将典,松崎 由理,石田 貴士,秋山 泰","エクソーム解析パイプラインの京コンピュータ上での大規模並列化","情報処理学会第38回バイオ情報学研究会","情報処理学会研究報告",,"  2014-BIO-38",,,2014,June
"Yutaka Akiyama","Development of an Ultra-Fast Computing Pipeline for Metagenome Analysis on Supercomputers","“Meeting Modern Life Science Challenges Through Computational Bioscience” CBRC Inauguration Symposium",,,,,,2014,June
"大上 雅史,下田 雄大,松崎由理,石田 貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム",,"研究報告数理モデル化と問題解決（MPS）","一般社団法人情報処理学会","Vol. 2014","No. 32","pp. 1-4",2014,June
"秋山 泰","大規模メタゲノム解析向け超並列相同性検索パイプラインの構築","「知の創出を支える次世代IT基盤拠点」 生命科学のビッグデータ研究会",,,,,,2014,Mar.
"伴兼弘,石田貴士,秋山泰","蛋白質-化合物ドッキングにおけるグリッドの分散配置による配座探索の改良","第37回バイオ情報学研究会","情報処理学会研究報告",,"vol. 2014-BIO-37","no. 4","pp. 1-7",2014,Mar.
"Shuji Suzuki,Takashi Ishida,Yutaka Akiyama","Accelerating identification of frequent k-mers in DNA sequences with GPU","GPU Technology Conference 2014 (GTC2014)",,,,"No. P4190",,2014,Mar.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Prediction of protein-protein interactions based on tertiary structures and transcription information","Biophysical Society 58th Annual Meeting",,,,,,2014,Feb.
"Yutaka Akiyama","Development of an Ultra-Fast Computing Pipeline for Metagenome Analysis on Supercomputers","KAUST bioinformatics seminar",,,,,,2014,Feb.
"Yutaka Akiyama","Development of an Ultra-Fast Computing Pipeline for Metagenome Analysis on TSUBAME2.5 and K-computer","The Japanese Extreme Big Data Projects Workshop",,,,,,2014,Feb.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Re-docking scheme to explore docking search space by using interaction profiles","Biophysical Society 58th Annual Meeting",,,,,,2014,Feb.
"大上雅史,下田雄大,松崎由理,内古閑伸之,鈴木脩司,石田貴士,秋山泰","MEGADOCK 4.0: mega-dock per dayへの道のり",,"生命情報科学若手の会 第5回研究会",,,,,2014,Feb.
"You H,Kim GE,Na CH,Lee S,Lee CJ,Cho KH,Akiyama Y,Ishida T,No KT.","An empirical model for gas phase acidity and basicity estimation",,"SAR and QSAR in Environmental Research",,"Vol. 25","No. 2","pp. 91-115",2014,Feb.
"Toshimoto K,Wakayama N,Kusama M,Maeda K,Sugiyama Y,Akiyama Y","In silico prediction of major drug clearance pathways by support vector machines with feature-selected descriptors",,"Drug Metabolism and Disposition",,"  42","  11","  1811-9",2014,
"Satoshi Matsuoka,Hitoshi Sato,Osamu Tatebe,Michihiro Koibuchi,Ikki Fujiwara,Shuji Suzuki,Masanori Kakuta,Takashi Ishida,Yutaka Akiyama,Toyotaro Suzumura,Koji Ueno,Hiroki Kanezashi,Takemasa Miyoshi.","Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year",,"Supercomputing frontiers and innovations",,"Vol. 1","No. 2","pp. 89-107",2014,
"渡部翔,鈴木脩司,石田貴士,秋山泰","GPGPUを用いた高速な配列相同性検索の圧縮アミノ酸を用いたアルゴリズム改良","第36回バイオ情報学研究会","情報処理学会研究報告",,"vol. 2013","no. 20","pp. 1-7",2013,Dec.
"杉浦典和,石田貴士,秋山泰,関嶋政和","de Bruijn Graphの分割によるVelvetの消費メモリの低減","第36回バイオ情報学研究会","情報処理学会研究報告",,"vol. 2013-BIO-36","no. 6","pp. 1-7",2013,Dec.
"小松祐城,石田貴士,秋山泰","拡張されたナイーブベイズを用いたメタゲノム配列の系統分類","第36回バイオ情報学研究会","情報処理学会研究報告",,"vol. 2013-BIO-36","no. 21","pp. 1-6",2013,Dec.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods",,"BMC Proceedings","BioMed Central","Volume 7","  Supplement 7","  S6",2013,Dec.
"石田 貴史,秋山泰,関嶋 政和,大野 一樹,折田 正弥","顧みられない熱帯病に対するIT創薬の現状 (今田治教授退任記念号・兵藤友博教授退任記念号)",,"立命館経営学","立命館大学","Vol. 52","No. 2","pp. 267-282",2013,Nov.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking","The 2013 Annual Conference of the Japanese Society for Bioinformatics (JSBi2013)",,,,,"  P077",2013,Nov.
"Yutaka Akiyama","Development of GPU-accelerated Bioinformatics Application Tools for supporting Drug Discovery: A Case Study in “Drugs for NTDs” Project","CMTPI-2013, 7-th International Symposium  ?  on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources",,,,,,2013,Oct.
"石田貴士,蓮実梢,伴兼弘,秋山泰","NTDs創薬ターゲットタンパク質選択のためのデータベースiNTRODBの開発","第54回日本熱帯医学会大会",,,,"No. p2-53",,2013,Oct.
"Takehiro Shimoda,Takashi Ishida,Shuji Suzuki,Masahito Ohue,Yutaka Akiyama","MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,"  P13",2013,Sept.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Takehiro Shimoda,Toshiyuki Sato,Takashi Ishida,Yutaka Akiyama","MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments",,"Source Code for Biology and Medicine","BioMed Central","Vol. 8","No. 1",,2013,Sept.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking","ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013)",,,,,"p. 667",2013,Sept.
"Takehiro Shimoda,Takashi Ishida,Shuji Suzuki,Masahito Ohue,Yutaka Akiyama","MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs","ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013)","Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013)","Association for Computing Machinery",,,"pp. 883-889",2013,Sept.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Re-docking scheme of protein-protein interactions for generating near-native interaction patterns in difficult docking cases","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,,2013,Sept.
"Hagiwara Y,Ohno K,Orita M,Koga R,Endo T,Akiyama Y,Sekijima M.","Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery",,"Curr Comput Aided Drug Des. 2013",,"Vol. 9","No. 3","pp. 396-401",2013,Sept.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Structure based protein-protein interaction network prediction of EGFR signaling related proteins using MEGADOCK","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,,2013,Sept.
"Takehiro Shimoda,Masahito Ohue,Yuri Matsuzaki,Takayuki Fujiwara,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments","ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013)",,,,,"p. 668",2013,Sept.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,"  P08",2013,Sept.
"小幡 康文,石田貴士,夏目 徹,秋山泰","タンデム質量分析ソフトウェアCoCoozoのマルチコアCPUとGPUを用いた高速化",,"研究報告数理モデル化と問題解決（MPS）","一般社団法人情報処理学会","Vol. 2013","No. 5","pp. 1-4",2013,July
"渡部翔,鈴木脩司,石田貴士,秋山泰","GPUを用いた配列相同性検索ツールGHOSTMの圧縮アミノ酸による高速化","GTC Workshop Japan 2013",,,,,,2013,July
"Yasufumi Obata,Takashi Ishida,Tohru Natsume,Yutaka Akiyama","Acceleration of Tandem Mass Spectrometry Analysis Software CoCoozo                   using Multi-core CPUs and Graphics Processing Units","The 2013 International Conference on Parallel and Distributed Processing Techniques and  Applications (PDPTA'13) Workshop on Mathematical Modeling  and Problem Solving",,,"Vol. I",,"pp. 149-154",2013,July
"Aizhen Ren,Takashi Ishida,Yutaka Akiyama","SDBP: An Easy-to-use R Program Package for Assessing Reliability of                   Estimated Phylogenetic Trees Based on the Speedy Double Bootstrap Method","The 2013 International Conference on Parallel and Distributed Processing Techniques and  Applications (PDPTA'13) Workshop on Mathematical Modeling  and Problem Solving",,,"Vol. I",,"pp. 143-148",2013,July
"下田雄大,石田貴士,鈴木脩司,大上雅史,秋山泰","MEGADOCK-GPU: GPUによるタンパク質間ドッキング計算の高速化",,"GTC Workshop Japan 2013",,,"No. 1",,2013,July
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints",,"PLOS ONE",,"Vol. 8","No. 7","  e69365",2013,July
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Yutaka Akiyama","Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis",,"Protein and Peptide Letters","Bentham Science","Volume 21","Issue 8","pp. 790-798",2013,July
"任 愛珍,石田貴士,秋山泰","SDBP: スピーディー・ダブルブートストラップ法に基づいた系統樹の信頼性評価のためのRパッケージ",,"研究報告数理モデル化と問題解決（MPS）","一般社団法人情報処理学会","Vol. 2013","No. 4","pp. 1-4",2013,July